I would like to run FSL and Freesurfer on my Linux compter. I have noticed that within Freesurfer I have a FSL directory. I have also visited the FSL website and noticed an entire downloadable version of FSL. I would like to be able to use my structural MPRAGE images that I have analyzed in Freesurfer and combine them with DTI images for ROI tractography and FA calculations. Do I need to download the version of FSL from the website? Secondly how should it be sourced so that FSL and Freesurfer are able to run together ( will I encounter any binary issues)? If you could respond with details. I am a novice to installing programs using a Linix machine. I am specifically talking about how to source the program and get it up and running.
Thanks